-N 100 hinder NanoCount accuracy?
callumparr opened this issue · comments
callumparr commented
I used the following command from minimap2
minimap2 -t 4 -ax map-ont -p 1.0 -N 100 -k14 -uf index/transcriptome_index.mmi
In the readme, it is recommended to use -N 10. Would having potentially more secondary alignments hinder the NanoCount accuracy?
Ideally, I would not like to remap all my samples again as just want to see a comparison of salmon vs NanoCount for each sample.
Josie Gleeson commented
Hi,
I wouldn't worry. NanoCount will filter out any secondary alignments that aren't very good/nearly as good as the primary alignment. So it shouldn't affect your results.
callumparr commented
Thank you 🙏